最佳匹配图中不正确正交图的完全刻画
Complete Characterization of Incorrect Orthology Assignments in Best Match Graphs
摘要：
基因组规模的同源性分配通常基于相互最佳匹配。在不存在水平基因转移（HGT）的情况下，每对直系同源物形成相互的最佳匹配。因此，不正确的正交分配在倒数最佳匹配图中总是误报。我们考虑重复/丢失的情况下，并表征明确的假阳性（U-FP）的正交分配，即，边缘的最佳匹配图（BMG），不能对应于任何基因树，解释BMG的直系同源。此外，我们提供了一个多项式时间的算法来确定所有的U-FP正交分配在BMG。仿真表明，至少$75\%$的所有不正确的正交分配可以检测到这种方式。所有结果仅依赖于BMG的结构，而不依赖于关于潜在基因或物种树的任何先验知识。
英文摘要：
Genome-scale orthology assignments are usually based on reciprocal best matches. In the absence of horizontal gene transfer (HGT), every pair of orthologs forms a reciprocal best match. Incorrect orthology assignments therefore are always false positives in the reciprocal best match graph. We consider duplication/loss scenarios and characterize unambiguous false-positive (u-fp) orthology assignments, that is, edges in the best match graphs (BMGs) that cannot correspond to orthologs for any gene tree that explains the BMG. Moreover, we provide a polynomial-time algorithm to identify all u-fp orthology assignments in a BMG. Simulations show that at least $75\%$ of all incorrect orthology assignments can be detected in this manner. All results rely only on the structure of the BMGs and not on any a priori knowledge about underlying gene or species trees.
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